7UIO
 
 | | Mediator-PIC Early (Composite Model) | | Descriptor: | ALANINE, ASPARTIC ACID, DNA (37-MER), ... | | Authors: | Gorbea Colon, J.J, Chen, S.-F, Tsai, K.L, Murakami, K. | | Deposit date: | 2022-03-29 | | Release date: | 2023-03-01 | | Last modified: | 2024-06-12 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural basis of a transcription pre-initiation complex on a divergent promoter.
Mol.Cell, 83, 2023
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7UI9
 | | Core Mediator-PICearly (Copy A) | | Descriptor: | DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB2, ... | | Authors: | Gorbea Colon, J.J, Chen, S.-F, Tsai, K.L, Murakami, K. | | Deposit date: | 2022-03-28 | | Release date: | 2023-02-15 | | Last modified: | 2023-03-08 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural basis of a transcription pre-initiation complex on a divergent promoter.
Mol.Cell, 83, 2023
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8GHA
 | | Hir3 Arm/Tail, Hir2 WD40, C-terminal Hpc2 | | Descriptor: | Histone promoter control protein 2, Histone transcription regulator 3, Protein HIR2 | | Authors: | Kim, H.J, Murakami, K. | | Deposit date: | 2023-03-09 | | Release date: | 2024-07-10 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (6.8 Å) | | Cite: | Structure of the Hir histone chaperone complex.
Mol.Cell, 2024
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8GHM
 | | Hir1 WD40 domains and Asf1/H3/H4 | | Descriptor: | Histone H3, Histone H4, Histone chaperone, ... | | Authors: | Kim, H.J, Murakami, K. | | Deposit date: | 2023-03-10 | | Release date: | 2024-07-10 | | Method: | ELECTRON MICROSCOPY (12 Å) | | Cite: | Structure of the Hir histone chaperone complex.
Mol.Cell, 2024
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6XKV
 | | R. capsulatus cyt bc1 with both FeS proteins in b position (CIII2 b-b) | | Descriptor: | Cytochrome b, Cytochrome c1, FE2/S2 (INORGANIC) CLUSTER, ... | | Authors: | Steimle, S, Van Eeuwen, T, Ozturk, Y, Kim, H.J, Braitbard, M, Selamoglu, N, Garcia, B.A, Schneidman-Duhovny, D, Murakami, K, Daldal, F. | | Deposit date: | 2020-06-27 | | Release date: | 2020-12-30 | | Last modified: | 2021-07-14 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Cryo-EM structures of engineered active bc 1 -cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes.
Nat Commun, 12, 2021
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6XKT
 | | R. capsulatus cyt bc1 with both FeS proteins in c position (CIII2 c-c) | | Descriptor: | Cytochrome b, Cytochrome c1, FE2/S2 (INORGANIC) CLUSTER, ... | | Authors: | Steimle, S, Van Eeuwen, T, Ozturk, Y, Kim, H.J, Braitbard, M, Selamoglu, N, Garcia, B.A, Schneidman-Duhovny, D, Murakami, K, Daldal, F. | | Deposit date: | 2020-06-27 | | Release date: | 2020-12-30 | | Last modified: | 2021-03-03 | | Method: | ELECTRON MICROSCOPY (3.75 Å) | | Cite: | Cryo-EM structures of engineered active bc 1 -cbb 3 type CIII 2 CIV super-complexes and electronic communication between the complexes.
Nat Commun, 12, 2021
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8DLF
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5U0P
 | | Cryo-EM structure of the transcriptional Mediator | | Descriptor: | Mediator complex subunit 10, Mediator complex subunit 11, Mediator complex subunit 14, ... | | Authors: | Tsai, K.-L, Yu, X, Gopalan, S, Chao, T.-C, Zhang, Y, Florens, L, Washburn, M.P, Murakami, K, Conaway, R.C, Conaway, J.W, Asturias, F. | | Deposit date: | 2016-11-26 | | Release date: | 2017-03-08 | | Last modified: | 2024-03-13 | | Method: | ELECTRON MICROSCOPY (4.4 Å) | | Cite: | Mediator structure and rearrangements required for holoenzyme formation.
Nature, 544, 2017
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5U0S
 | | Cryo-EM structure of the Mediator-RNAPII complex | | Descriptor: | Mediator complex subunit 10, Mediator complex subunit 11, Mediator complex subunit 14, ... | | Authors: | Tsai, K.-L, Yu, X, Gopalan, S, Chao, T.-C, Zhang, Y, Florens, L, Washburn, M.P, Murakami, K, Conaway, R.C, Conaway, J.W, Asturias, F. | | Deposit date: | 2016-11-26 | | Release date: | 2017-03-08 | | Last modified: | 2020-01-01 | | Method: | ELECTRON MICROSCOPY (7.8 Å) | | Cite: | Mediator structure and rearrangements required for holoenzyme formation.
Nature, 544, 2017
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1I6V
 | | THERMUS AQUATICUS CORE RNA POLYMERASE-RIFAMPICIN COMPLEX | | Descriptor: | DNA-DIRECTED RNA POLYMERASE, MAGNESIUM ION, RIFAMPICIN, ... | | Authors: | Campbell, E.A, Korzheva, N, Mustaev, A, Murakami, K, Goldfarb, A, Darst, S.A. | | Deposit date: | 2001-03-05 | | Release date: | 2001-04-18 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Structural mechanism for rifampicin inhibition of bacterial rna polymerase.
Cell(Cambridge,Mass.), 104, 2001
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7KPW
 | | Structure of the H-lobe of yeast CKM | | Descriptor: | Mediator of RNA polymerase II transcription subunit 12 | | Authors: | Li, Y.C, Chao, T.C, Kim, H.J, Cholko, T, Chen, S.F, Nakanishi, K, Chang, C.E, Murakami, K, Garcia, B.A, Boyer, T.G, Tsai, K.L. | | Deposit date: | 2020-11-12 | | Release date: | 2021-01-27 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (4.9 Å) | | Cite: | Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Sci Adv, 7, 2021
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7KPX
 | | Structure of the yeast CKM | | Descriptor: | Mediator of RNA polymerase II transcription subunit 12, Mediator of RNA polymerase II transcription subunit 13, Meiotic mRNA stability protein kinase SSN3, ... | | Authors: | Li, Y.C, Chao, T.C, Kim, H.J, Cholko, T, Chen, S.F, Nakanishi, K, Chang, C.E, Murakami, K, Garcia, B.A, Boyer, T.G, Tsai, K.L. | | Deposit date: | 2020-11-12 | | Release date: | 2021-01-27 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (4.4 Å) | | Cite: | Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Sci Adv, 7, 2021
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7KPV
 | | Structure of kinase and Central lobes of yeast CKM | | Descriptor: | Mediator of RNA polymerase II transcription subunit 12, Mediator of RNA polymerase II transcription subunit 13, Meiotic mRNA stability protein kinase SSN3, ... | | Authors: | Li, Y.C, Chao, T.C, Kim, H.J, Cholko, T, Chen, S.F, Nakanishi, K, Chang, C.E, Murakami, K, Garcia, B.A, Boyer, T.G, Tsai, K.L. | | Deposit date: | 2020-11-12 | | Release date: | 2021-01-27 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module.
Sci Adv, 7, 2021
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7ML0
 | | RNA polymerase II pre-initiation complex (PIC1) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML1
 | | RNA polymerase II pre-initiation complex (PIC2) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (4 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML4
 | | RNA polymerase II initially transcribing complex (ITC) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-03-09 | | Method: | ELECTRON MICROSCOPY (3.1 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML3
 | | General transcription factor TFIIH (weak binding) | | Descriptor: | BJ4_G0050160.mRNA.1.CDS.1, General transcription and DNA repair factor IIH, General transcription and DNA repair factor IIH helicase subunit XPB, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (7.6 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7ML2
 | | RNA polymerase II pre-initiation complex (PIC3) | | Descriptor: | BJ4_G0004860.mRNA.1.CDS.1, BJ4_G0050160.mRNA.1.CDS.1, DNA-directed RNA polymerase II subunit RPB11, ... | | Authors: | Yang, C, Fujiwara, R, Kim, H.J, Gorbea Colon, J.J, Steimle, S, Garcia, B.A, Murakami, K. | | Deposit date: | 2021-04-27 | | Release date: | 2022-02-02 | | Last modified: | 2022-02-16 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MEI
 | | Composite structure of EC+EC | | Descriptor: | DNA (74-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-06 | | Release date: | 2022-03-02 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MKA
 | | Structure of EC+EC (leading EC-focused) | | Descriptor: | DNA (40-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-22 | | Release date: | 2022-04-27 | | Last modified: | 2023-05-17 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7MK9
 | | Complex structure of trailing EC of EC+EC (trailing EC-focused) | | Descriptor: | DNA (40-MER), DNA-directed RNA polymerase II subunit RPB11, DNA-directed RNA polymerase II subunit RPB3, ... | | Authors: | Yang, C, Murakami, K. | | Deposit date: | 2021-04-22 | | Release date: | 2022-04-27 | | Last modified: | 2023-05-17 | | Method: | ELECTRON MICROSCOPY (3.54 Å) | | Cite: | Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II.
Mol.Cell, 82, 2022
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7JTH
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7K04
 | | Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening | | Descriptor: | CALCIUM ION, DNA repair helicase RAD25, DNA repair helicase RAD3, ... | | Authors: | van Eeuwen, T, Min, J.H, Murakami, K. | | Deposit date: | 2020-09-03 | | Release date: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (9.25 Å) | | Cite: | Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Nat Commun, 12, 2021
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7K01
 | | Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex | | Descriptor: | DNA repair helicase RAD25, DNA repair helicase RAD3, General transcription and DNA repair factor IIH subunit SSL1, ... | | Authors: | van Eeuwen, T, Min, J.H, Murakami, K. | | Deposit date: | 2020-09-02 | | Release date: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Nat Commun, 12, 2021
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7M2U
 | | Nucleotide Excision Repair complex TFIIH Rad4-33 | | Descriptor: | CALCIUM ION, DNA repair helicase RAD25, DNA repair helicase RAD3, ... | | Authors: | van Eeuwen, T, Murakami, K. | | Deposit date: | 2021-03-17 | | Release date: | 2021-07-28 | | Method: | ELECTRON MICROSCOPY (8.2 Å) | | Cite: | Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Nat Commun, 12, 2021
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